Working on doxygen support.

CMakeLists.txt

 cmake_minimum_required(VERSION 2.8.5)
 
-set(CMAKE_MODULE_PATH    ${CMAKE_SOURCE_DIR}/cmake/modules)
+set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules)
 set(CMAKE_TOOLCHAIN_FILE ${CMAKE_SOURCE_DIR}/cmake/toolchains/Arduino.cmake)
 
 # modify flags from default toolchain flags
@@ -31,6 +31,7 @@ set(APPLICATION_VERSION "${APPLICATION_VERSION_MAJOR}.${APPLICATION_VERSION_MINO
 
 # macros
 include(MacroEnsureOutOfSourceBuild)
+include(UseDoxygen)
 
 # disallow in-source build
 macro_ensure_out_of_source_build("${PROJECT_NAME} requires an out of source build.

cmake/modules/UseDoxygen.cmake

+# - Run Doxygen
+#
+# Adds a doxygen target that runs doxygen to generate the html
+# and optionally the LaTeX API documentation.
+# The doxygen target is added to the doc target as a dependency.
+# i.e.: the API documentation is built with:
+#  make doc
+#
+# USAGE: GLOBAL INSTALL
+#
+# Install it with:
+#  cmake ./ && sudo make install
+# Add the following to the CMakeLists.txt of your project:
+#  include(UseDoxygen OPTIONAL)
+# Optionally copy Doxyfile.in in the directory of CMakeLists.txt and edit it.
+#
+# USAGE: INCLUDE IN PROJECT
+#
+#  set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
+#  include(UseDoxygen)
+# Add the Doxyfile.in and UseDoxygen.cmake files to the projects source directory.
+#
+#
+# CONFIGURATION
+#
+# To configure Doxygen you can edit Doxyfile.in and set some variables in cmake.
+# Variables you may define are:
+#  DOXYFILE_SOURCE_DIR - Path where the Doxygen input files are.
+#  	Defaults to the current source directory.
+#  DOXYFILE_EXTRA_SOURCES - Additional source diretories/files for Doxygen to scan.
+#  	The Paths should be in double quotes and separated by space. e.g.:
+#  	 "${CMAKE_CURRENT_BINARY_DIR}/foo.c" "${CMAKE_CURRENT_BINARY_DIR}/bar/"
+#  
+#  DOXYFILE_OUTPUT_DIR - Path where the Doxygen output is stored.
+#  	Defaults to "${CMAKE_CURRENT_BINARY_DIR}/doc".
+#  
+#  DOXYFILE_LATEX - ON/OFF; Set to "ON" if you want the LaTeX documentation
+#  	to be built.
+#  DOXYFILE_LATEX_DIR - Directory relative to DOXYFILE_OUTPUT_DIR where
+#  	the Doxygen LaTeX output is stored. Defaults to "latex".
+#  
+#  DOXYFILE_HTML_DIR - Directory relative to DOXYFILE_OUTPUT_DIR where
+#  	the Doxygen html output is stored. Defaults to "html".
+#
+
+#
+#  Copyright (c) 2009, 2010, 2011 Tobias Rautenkranz <tobias@rautenkranz.ch>
+#
+#  Redistribution and use is allowed according to the terms of the New
+#  BSD license.
+#  For details see the accompanying COPYING-CMAKE-SCRIPTS file.
+#
+
+macro(usedoxygen_set_default name value type docstring)
+	if(NOT DEFINED "${name}")
+		set("${name}" "${value}" CACHE "${type}" "${docstring}")
+	endif()
+endmacro()
+
+find_package(Doxygen)
+
+if(DOXYGEN_FOUND)
+	find_file(DOXYFILE_IN "Doxyfile.in"
+			PATHS "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_ROOT}/Modules/"
+			NO_DEFAULT_PATH
+			DOC "Path to the doxygen configuration template file")
+	set(DOXYFILE "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
+	include(FindPackageHandleStandardArgs)
+	find_package_handle_standard_args(DOXYFILE_IN DEFAULT_MSG "DOXYFILE_IN")
+endif()
+
+if(DOXYGEN_FOUND AND DOXYFILE_IN_FOUND)
+	usedoxygen_set_default(DOXYFILE_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/doc"
+		PATH "Doxygen output directory")
+	usedoxygen_set_default(DOXYFILE_HTML_DIR "html"
+		STRING "Doxygen HTML output directory")
+	usedoxygen_set_default(DOXYFILE_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}"
+		PATH "Input files source directory")
+	usedoxygen_set_default(DOXYFILE_EXTRA_SOURCE_DIRS ""
+		STRING "Additional source files/directories separated by space")
+	set(DOXYFILE_SOURCE_DIRS "\"${DOXYFILE_SOURCE_DIR}\" ${DOXYFILE_EXTRA_SOURCES}")
+
+	usedoxygen_set_default(DOXYFILE_LATEX YES BOOL "Generate LaTeX API documentation" OFF)
+	usedoxygen_set_default(DOXYFILE_LATEX_DIR "latex" STRING "LaTex output directory")
+
+	mark_as_advanced(DOXYFILE_OUTPUT_DIR DOXYFILE_HTML_DIR DOXYFILE_LATEX_DIR
+		DOXYFILE_SOURCE_DIR DOXYFILE_EXTRA_SOURCE_DIRS DOXYFILE_IN)
+
+
+	set_property(DIRECTORY 
+		APPEND PROPERTY
+		ADDITIONAL_MAKE_CLEAN_FILES
+		"${DOXYFILE_OUTPUT_DIR}/${DOXYFILE_HTML_DIR}")
+
+	add_custom_target(doxygen
+		COMMAND "${DOXYGEN_EXECUTABLE}"
+			"${DOXYFILE}" 
+		COMMENT "Writing documentation to ${DOXYFILE_OUTPUT_DIR}..."
+		WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+
+	set(DOXYFILE_DOT "NO")
+	if(DOXYGEN_DOT_EXECUTABLE)
+		set(DOXYFILE_DOT "YES")
+	endif()
+
+	## LaTeX
+	set(DOXYFILE_PDFLATEX "NO")
+
+	set_property(DIRECTORY APPEND PROPERTY
+		ADDITIONAL_MAKE_CLEAN_FILES
+		"${DOXYFILE_OUTPUT_DIR}/${DOXYFILE_LATEX_DIR}")
+
+	if(DOXYFILE_LATEX STREQUAL "ON")
+		set(DOXYFILE_GENERATE_LATEX "YES")
+		find_package(LATEX)
+		find_program(DOXYFILE_MAKE make)
+		mark_as_advanced(DOXYFILE_MAKE)
+		if(LATEX_COMPILER AND MAKEINDEX_COMPILER AND DOXYFILE_MAKE)
+			if(PDFLATEX_COMPILER)
+				set(DOXYFILE_PDFLATEX "YES")
+			endif()
+
+			add_custom_command(TARGET doxygen
+				POST_BUILD
+				COMMAND "${DOXYFILE_MAKE}"
+				COMMENT	"Running LaTeX for Doxygen documentation in ${DOXYFILE_OUTPUT_DIR}/${DOXYFILE_LATEX_DIR}..."
+				WORKING_DIRECTORY "${DOXYFILE_OUTPUT_DIR}/${DOXYFILE_LATEX_DIR}")
+		else()
+			set(DOXYGEN_LATEX "NO")
+		endif()
+	else()
+		set(DOXYFILE_GENERATE_LATEX "NO")
+	endif()
+
+
+	configure_file("${DOXYFILE_IN}" "${DOXYFILE}" @ONLY)
+
+	get_target_property(DOC_TARGET doc TYPE)
+	if(NOT DOC_TARGET)
+		add_custom_target(doc)
+	endif()
+
+	add_dependencies(doc doxygen)
+endif()